The long-term goal of the proposed research is to better understand the molecular mechanisms that regulate RNA polymerase I transcription of ribosomal RNA. This rRNA becomes the major structural and functional component of ribosomes and its rate of synthesis determines the rate of ribosome biogenesis, which in turn is directly correlated with cell growth rate. Thus it is of great importance to understand this process so as to understand the increased growth characteristic of cancer cells. Indeed, many cancer therapeutics that target rapidly growing cells function in part by decreasing RNA polymerase I transcription and new drugs are being tested that specifically target this process. Huge advances have been made in structural and functional analyses of the polymerase itself and of additional factors that participate in making ribosomal RNA, yet many important questions remain unanswered. The Beyer laboratory contributes a unique in vivo approach to this research effort by using electron microscopy to directly visualize active rRNA genes released from growing cells. The Miller chromatin spreading method allows high-resolution analysis of many individual genes as well as analysis of the gene population in many individual nucleoli. Using Saccharomyces cerevisiae as a model system, rRNA genes are visualized in the presence and absence of key regulatory proteins (i.e., in appropriate mutant strains) to determine how these proteins affect rRNA synthesis at the individual gene level in living cells. Changes or defects in transcription initiation, elongation, termination, processing of nascent transcripts, chromatin structure and template topology can be discerned and distinguished, as well as any coupling between these processes. Quantitative analysis of many individual genes allows determination of statistically significant changes and provides mechanistic insight, such as distinction between elongation factors that contribute to recognition of intrinsic pause sites and those that help polymerases transit such sites. The specific goals of this project are (1) to characterize the in vivo function of RNA polymerase I subunits in rRNA transcription and transcription-coupled RNA processing, (2) to characterize the in vivo function of two elongation factors, Spt5 and FACT, in rRNA transcription and transcription-coupled RNA processing, and (3) to investigate transcription termination by RNA polymerase I and identify contributions from nascent transcript degradation, intrinsic pause sites, protein roadblocks and RNA cleavage activity intrinsic to the polymerase. The information gained by direct visualization of active genes from living cells is extremely valuable when combined with genetic and biochemical analyses from other investigators, and together provide a much more complete picture of the regulation of ribosomal RNA synthesis by RNA polymerase I.